Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: Highlights protein analysis applications such as protein-related drug activity comparison Incorporates salient case studies illustrating how to apply the methods outlined in the book Tackles the complex relationship between proteins from a systems biology point of view Relates the topic to other emerging technologies such as data mining and visualization Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.

Algorithmic and Artificial Intelligence Methods for Protein BioinformaticsAn in-depth look at the latest research, methods, and applications in the field of protein bioinformaticsThis book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems.Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics:* Highlights protein analysis applications such as protein-related drug activity comparison* Incorporates salient case studies illustrating how to apply the methods outlined in the book* Tackles the complex relationship between proteins from a systems biology point of view* Relates the topic to other emerging technologies such as data mining and visualization* Includes many tables and illustrations demonstrating concepts and performance figuresAlgorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.

PREFACE ixCONTRIBUTORS xvI FROM PROTEIN SEQUENCE TO STRUCTURE1 EMPHASIZING THE ROLE OF PROTEINS IN CONSTRUCTION OF THEDEVELOPMENTAL GENETIC TOOLKIT IN PLANTS 3Anamika Basu and Anasua Sarkar2 PROTEIN SEQUENCE MOTIF INFORMATION DISCOVERY 41Bernard Chen3 IDENTIFYING CALCIUM BINDING SITES IN PROTEINS 57Hui Liu and Hai Deng4 REVIEW OF IMBALANCED DATA LEARNING FOR PROTEIN METHYLATIONPREDICTION 71Zejin Ding and Yan-Qing Zhang5 ANALYSIS AND PREDICTION OF PROTEIN POSTTRANSLATIONALMODIFICATION SITES 91Jianjiong Gao, Qiuming Yao, Curtis Harrison Bollinger, and DongXuII PROTEIN ANALYSIS AND PREDICTION6 PROTEIN LOCAL STRUCTURE PREDICTION 109Wei Zhong, Jieyue He, Robert W. Harrison, Phang C. Tai, and YiPan7 PROTEIN STRUCTURAL BOUNDARY PREDICTION 125Gulsah Altun8 PREDICTION OF RNA BINDING SITES IN PROTEINS 153Zhi-Ping Liu and Luonan Chen9 ALGORITHMIC FRAMEWORKS FOR PROTEIN DISULFIDE CONNECTIVITYDETERMINATION 171Rahul Singh, William Murad, and Timothy Lee10 PROTEIN CONTACT ORDER PREDICTION: UPDATE 205Yi Shi, Jianjun Zhou, David S. Wishart, and Guohui Lin11 PROGRESS IN PREDICTION OF OXIDATION STATES OF CYSTEINES VIACOMPUTATIONAL APPROACHES 217Aiguo Du, Hui Liu, Hai Deng, and Yi Pan12 COMPUTATIONAL METHODS IN CRYOELECTRON MICROSCOPY 3D STRUCTURERECONSTRUCTION 231Fa Zhang, Xiaohua Wan, and Zhiyong LiuIII PROTEIN STRUCTURE ALIGNMENT AND ASSESSMENT13 FUNDAMENTALS OF PROTEIN STRUCTURE ALIGNMENT 255Mark Brandt, Allen Holder, and Yosi Shibberu14 DISCOVERING 3D PROTEIN STRUCTURES FOR OPTIMAL STRUCTUREALIGNMENT 281TomáS Novosád, Václav SnáSel,Ajith Abraham, and Jack Y. Yang15 ALGORITHMIC METHODOLOGIES FOR DISCOVERY OF NONSEQUENTIALPROTEIN STRUCTURE SIMILARITIES 299Bhaskar DasGupta, Joseph Dundas, and Jie Liang16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURECLASSES AND FUNCTIONS 317Zu-Guo Yu, Vo Anh, Jian-Yi Yang, and Shao-Ming Zhu17 PROTEIN TERTIARY MODEL ASSESSMENT 339Anjum Chida, Robert W. Harrison, and Yan-Qing ZhangIV PROTEIN-PROTEIN ANALYSIS OF BIOLOGICALNETWORKS18 NETWORK ALGORITHMS FOR PROTEIN INTERACTIONS 357Suely Oliveira19 IDENTIFYING PROTEIN COMPLEXES FROM PROTEIN-PROTEININTERACTION NETWORKS 377Jianxin Wang, Min Li, and Xiaoqing Peng20 PROTEIN FUNCTIONAL MODULE ANALYSIS WITH PROTEIN-PROTEININTERACTION (PPI) NETWORKS 393Lei Shi, Xiujuan Lei, and Aidong Zhang21 EFFICIENT ALIGNMENTS OF METABOLIC NETWORKS WITH BOUNDEDTREEWIDTH 413Qiong Cheng, Piotr Berman, Robert W. Harrison, and AlexanderZelikovsky22 PROTEIN-PROTEIN INTERACTION NETWORK ALIGNMENT:ALGORITHMS AND TOOLS 431Valeria FiondaV APPLICATION OF PROTEIN BIOINFORMATICS23 PROTEIN-RELATED DRUG ACTIVITY COMPARISON USING SUPPORT VECTORMACHINES 451Wei Zhong and Jieyue He24 FINDING REPETITIONS IN BIOLOGICAL NETWORKS: CHALLENGES,TRENDS, AND APPLICATIONS 461Simona E. Rombo25 MeTaDoR: ONLINE RESOURCE AND PREDICTION SERVER FOR MEMBRANETARGETING PERIPHERAL PROTEINS 481Nitin Bhardwaj, Morten Källberg, Wonhwa Cho, and HuiLu26 BIOLOGICAL NETWORKS-BASED ANALYSIS OF GENE EXPRESSIONSIGNATURES 495Gang Chen and Jianxin WangINDEX 507